Insect Data Analysis

This is a repository of R scripts and datasets used to explore, clean and visualise insect occurrence records, particularly those found in Sentosa, Singapore. It was created as part of a project to understand the potential of using citizen science data to map the distribution of species within the island.

Created for the Ecological Adaptations Lab at Yale-NUS College in 2021.

SECTION 1. Project Structure

The folders and its contents are structured as follows.

sentosa-insects
│   README.md
│   sentosa-insects.Rproj
│   start.R
│
├───code
│       01-sentosa-insect-inat-exploration.R
│       02-sentosa-insect-inat-cleaning.R
│       03-sentosa-insect-inat-visualisation.R
│       04-sentosa-insect-inat-leaflet.R
│       05-bees-leaflet.R
|	functions.R
│
├───data
│       processed.zip
│       qgis-file.zip
│       raw.zip
│
├───docs
│       20210511-labmeeting.pptx
│
├───images
│   ├───charts
│   │       inaturalist-sentosa-topusers.png
│   │       inaturalist-sentosa-yearly-user-contributions.png
│   │       inaturalist-sentosa-yearly-user-contributions_no-anomaly.png
│   │       orders-families-sentosa-breakdown_black.png
│   │       orders-families-sentosa-breakdown_colored.png
│   │       sentosa-insect-species-top10.png
│   │       sentosa-insect-species-top15.png
│   │
│   └───insects
│           Abisara saturata.jpg
│
└───maps
        order-maps.zip
        species-maps.zip

SECTION 2. How To Use

Accessing the code and datasets

1. Unzip raw.zip and processed.zip in the data folder, which contains the occurrence data as well as shapefiles of Singapore's maps, some of which I have used for cleaning the observations.

   • The qgis-file.zip contains a QGIS file I had put together to label polygons of Singapore's islands with their names, as I needed them to figure out which insect observations were in Sentosa. No need to open it as the labelled polygons have been saved into data\raw.

2. Click on sentosa-insects.Rproj to open the project in your RStudio with all its associated files loaded.

3. The R scripts in the code folder contains the progression of my data clean up and visualisation, sequentially from file 01 to 05. If you would like to run them, consider doing so segment by segment and going through the comments in each file.

   • Each of these R scripts has source("start.R") as their first line, where running it loads the packages and file paths needed for the project from start.R.
   • functions.R are generalised functions to create Leaflet maps by order and species, and can be run independently of the other scripts.

4. Please ensure the working directories are accurate with respect to your device as you're running the code. E.g. data isn't nestled within a subfolder data after you've unzipped it.

Using the documentation and output (maps and images)

Folder	Usage
docs	Any documentation made during the data analysis. Contains slides and a report (TBC).
images\charts	Plots created and saved from the data visualisation process in the R script starting with 03.
images\insects	This is where images of insects downloaded from iNaturalist get saved to, also as part of the R script starting with 03. It currently contains one sample image, but more can be downloaded automatically by running a function within the 03 file. Refer to the script for more details.
maps	Interactable HTML maps created from the R scripts 04 and 05. Contains maps by orders and species.

SECTION 3. References

Dataset and Image Sources

• DIVA-GIS for Singapore's shapefiles
• Richards, Dan; Gaw, Leon Yan-Feng; Yee, Alex T.K. (2019): A high-resolution map of Singapore’s terrestrial ecosystems. figshare. Dataset. for Singapore's maps
• iNaturalist for insect occurrence data. Accessed on 31 May 2021 with the query quality_grade=research&identifications=any&iconic_taxa%5B%5D=Insecta&place_id=6734.
• NCBI Taxonomy Database for the taxonomy information of species

Code References

• R Graph Gallery for charts and their code